Cryo-EM structure of PTH-PTH1R-Gq (upright state)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9jr2
Q-score: 0.492
Sano FK, Kobayashi K, Kawakami K, Akasaka H, Kobayashi TA, Tanaka T, Okamoto HH, Hirano H, Kusakizako T, Shihoya W, Kise Y, Itoh Y, Ishitani R, Okada Y, Inoue A, Nureki O
To Be Published
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Gprotein gamma-2 (Complex from Bos taurus)
- Mini-g (Complex from Homo sapiens)
- Parathyroid hormone (4 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus rattus)
- Scfv16 (27 kDa, Protein from Mus musculus)
- Parathyroid hormone/parathyroid hormone-related peptide receptor (63 kDa, Protein from Homo sapiens)
- Parathyroid hormone 1 receptor (Complex from Homo sapiens)
- Gprotein beta-1 (Complex from Rattus rattus)
- Parathyroid hormone (Complex from Homo sapiens)
- Scfv16 (Complex from Mus musculus)
- Water (18 Da, Ligand)
- Guanine nucleotide-binding protein g(q) subunit alpha-1 (minigq) (27 kDa, Protein from Homo sapiens)
- Pth-pth1r-gq complex (Complex)
Cryo-EM structure of PTH-PTH1R-Gq (tilted state)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9jr3
Q-score: 0.487
Sano FK, Kobayashi K, Kawakami K, Akasaka H, Kobayashi TA, Tanaka T, Okamoto HH, Hirano H, Kusakizako T, Shihoya W, Kise Y, Itoh Y, Ishitani R, Okada Y, Inoue A, Nureki O
To Be Published
- Pth (Complex from Homo sapiens)
- Minigq (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit gamma-2 (Complex from Bos taurus)
- Pth1r (Complex from Homo sapiens)
- Parathyroid hormone (4 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus rattus)
- Scfv16 (27 kDa, Protein from Mus musculus)
- Parathyroid hormone/parathyroid hormone-related peptide receptor (63 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (minigq) (27 kDa, Protein from Homo sapiens)
- Scfv16 (Complex from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (Complex from Rattus rattus)
- Water (18 Da, Ligand)
- Pth-pth1r-gq complex (Complex)
SpCas9-MMLV RT-pegRNA-target DNA complex (termination)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8wus
Q-score: 0.454
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) 631 pp. 224-231 [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (40-mer) (12 kDa, DNA from Streptococcus pyogenes)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (5'-d(*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Rna (115-mer) (37 kDa, RNA from Streptococcus pyogenes)
SpCas9-MMLV RT-pegRNA-target DNA complex (initiation)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8wut
Q-score: 0.364
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) 631 pp. 224-231 [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (5'-d(*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Dna/rna (35-mer) (10 kDa, Macromolecule from Streptococcus pyogenes)
- Rna (115-mer) (37 kDa, RNA from Streptococcus pyogenes)
SpCas9-pegRNA-target DNA complex (pre-initiation)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8wuu
Q-score: 0.392
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) 631 pp. 224-231 [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Dna (5'-d(*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Spcas9-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Rna (137-mer) (44 kDa, RNA from Streptococcus pyogenes)
- Dna (34-mer) (10 kDa, DNA from Streptococcus pyogenes)
SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 16-nt)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8wuv
Q-score: 0.354
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) 631 pp. 224-231 [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Dna (5'-d(*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Dna (50-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Rna (137-mer) (44 kDa, RNA from Streptococcus pyogenes)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 28-nt)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8ygj
Q-score: 0.354
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) 631 pp. 224-231 [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (5'-d(p*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (62-mer) (19 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Rna (137-mer) (44 kDa, RNA from Streptococcus pyogenes)
Small subunit of yeast mitochondrial ribosome in complex with METTL17/Rsm22.
Resolution: 2.57 Å
EM Method: Single-particle
Fitted PDBs: 8om2
Q-score: 0.602
Ast T, Itoh Y, Sadre S, McCoy JG, Namkoong G, Wengrod JC, Chicherin I, Joshi PR, Kamenski P, Suess DLM, Amunts A, Mootha VK
Mol Cell (2024) 84 pp. 359- [ DOI: doi:10.1016/j.molcel.2023.12.016 Pubmed: 38199006 ]
- 37s ribosomal protein s26, mitochondrial (30 kDa, Protein from Saccharomyces cerevisiae)
- Mitochondrial 37s ribosomal protein s27 (12 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein rsm18, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp51, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s25, mitochondrial (30 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s35, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- Protein fyv4, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s24, mitochondrial (37 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s16, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein sws2, mitochondrial (16 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp21, mitochondrial (20 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s18, mitochondrial (24 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s28, mitochondrial (33 kDa, Protein from Saccharomyces cerevisiae)
- Mitochondrial mrna-processing protein cox24 (12 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp4, mitochondrial (44 kDa, Protein from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- 37s ribosomal protein mrp17, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s8, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 37s ribosomal protein s10, mitochondrial (23 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- 37s ribosomal protein mrp13, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s17, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 37s ribosomal protein s5, mitochondrial (34 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp10, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- Small subunit of mitochondrial ribosome in complex with mettl17/rsm22 (Complex from Saccharomyces cerevisiae)
- 15s mitochondrial rrna (528 kDa, RNA from Saccharomyces cerevisiae)
- 37s ribosomal protein s23, mitochondrial (50 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- 37s ribosomal protein nam9, mitochondrial (56 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein pet123, mitochondrial (36 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s9, mitochondrial (31 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s19, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s12, mitochondrial (16 kDa, Protein from Saccharomyces cerevisiae)
- Ribosomal protein var1, mitochondrial (47 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp1, mitochondrial (36 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- 3-hydroxyisobutyryl-coa hydrolase, mitochondrial (56 kDa, Protein from Saccharomyces cerevisiae)
- Probable s-adenosyl-l-methionine-dependent rna methyltransferase rsm22, mitochondrial (72 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s7, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp2, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
Small subunit of yeast mitochondrial ribosome in complex with IF3/Aim23.
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 8om3
Q-score: 0.564
Ast T, Itoh Y, Sadre S, McCoy JG, Namkoong G, Wengrod JC, Chicherin I, Joshi PR, Kamenski P, Suess DLM, Amunts A, Mootha VK
Mol Cell (2024) 84 pp. 359- [ DOI: doi:10.1016/j.molcel.2023.12.016 Pubmed: 38199006 ]
- Small subunit of mitochondrial ribosome in complex with if3/aim23 (Complex from Saccharomyces cerevisiae)
- 37s ribosomal protein s26, mitochondrial (30 kDa, Protein from Saccharomyces cerevisiae)
- Mitochondrial 37s ribosomal protein s27 (12 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein rsm18, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp51, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s25, mitochondrial (30 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s8, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- Protein fyv4, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s24, mitochondrial (37 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s35, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s16, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein sws2, mitochondrial (16 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp21, mitochondrial (20 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s18, mitochondrial (24 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s28, mitochondrial (33 kDa, Protein from Saccharomyces cerevisiae)
- Altered inheritance of mitochondria protein 23, mitochondrial (42 kDa, Protein from Saccharomyces cerevisiae)
- Mitochondrial mrna-processing protein cox24 (12 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp4, mitochondrial (44 kDa, Protein from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- 37s ribosomal protein mrp17, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 37s ribosomal protein s10, mitochondrial (23 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- 37s ribosomal protein mrp13, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s17, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s5, mitochondrial (34 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp10, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- 15s mitochondrial rrna (528 kDa, RNA from Saccharomyces cerevisiae)
- 37s ribosomal protein s23, mitochondrial (50 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- 37s ribosomal protein nam9, mitochondrial (56 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein pet123, mitochondrial (36 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s9, mitochondrial (31 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s19, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s12, mitochondrial (16 kDa, Protein from Saccharomyces cerevisiae)
- Ribosomal protein var1, mitochondrial (47 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp1, mitochondrial (36 kDa, Protein from Saccharomyces cerevisiae)
- 3-hydroxyisobutyryl-coa hydrolase, mitochondrial (56 kDa, Protein from Saccharomyces cerevisiae)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 37s ribosomal protein s7, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp2, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
Small subunit of yeast mitochondrial ribosome.
Resolution: 2.32 Å
EM Method: Single-particle
Fitted PDBs: 8om4
Q-score: 0.654
Ast T, Itoh Y, Sadre S, McCoy JG, Namkoong G, Wengrod JC, Chicherin I, Joshi PR, Kamenski P, Suess DLM, Amunts A, Mootha VK
Mol Cell (2024) 84 pp. 359- [ DOI: doi:10.1016/j.molcel.2023.12.016 Pubmed: 38199006 ]
- 37s ribosomal protein s26, mitochondrial (30 kDa, Protein from Saccharomyces cerevisiae)
- Mitochondrial 37s ribosomal protein s27 (12 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein rsm18, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp51, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s25, mitochondrial (30 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s8, mitochondrial (17 kDa, Protein from Saccharomyces cerevisiae)
- Protein fyv4, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s24, mitochondrial (37 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s35, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s16, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein sws2, mitochondrial (16 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp21, mitochondrial (20 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s18, mitochondrial (24 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s28, mitochondrial (33 kDa, Protein from Saccharomyces cerevisiae)
- Mitochondrial mrna-processing protein cox24 (12 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp4, mitochondrial (44 kDa, Protein from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- 37s ribosomal protein mrp17, mitochondrial (15 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 37s ribosomal protein s10, mitochondrial (23 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- 37s ribosomal protein mrp13, mitochondrial (39 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s17, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s5, mitochondrial (34 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp10, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- 15s mitochondrial rrna (528 kDa, RNA from Saccharomyces cerevisiae)
- 37s ribosomal protein s23, mitochondrial (50 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- 37s ribosomal protein nam9, mitochondrial (56 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein pet123, mitochondrial (36 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s9, mitochondrial (31 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s19, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein s12, mitochondrial (16 kDa, Protein from Saccharomyces cerevisiae)
- Ribosomal protein var1, mitochondrial (47 kDa, Protein from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp1, mitochondrial (36 kDa, Protein from Saccharomyces cerevisiae)
- 3-hydroxyisobutyryl-coa hydrolase, mitochondrial (56 kDa, Protein from Saccharomyces cerevisiae)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 37s ribosomal protein s7, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- Small subunit of mitochondrial ribosome (Complex from Saccharomyces cerevisiae)
- 37s ribosomal protein mrp2, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)